Spatial Single Cell Analysis in Python

R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics

High dimensional weighted gene co-expression network analysis

Tools for computational pathology

Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics

DANCE: a deep learning library and benchmark platform for single-cell analysis

Integrating histology and spatial transcriptomics - NeurIPS 2024

Spatiotemporal modeling of spatial transcriptomics

SpaGCN: Integrating gene expression, spatial location and histology to identify spatial domains and spatially variable genes by graph convolutional network

Technology-invariant pipeline for spatial omics analysis that scales to millions of cells (Xenium / Visium HD / MERSCOPE / CosMx / PhenoCycler / MACSima / etc)

Python package to perform enrichment analysis from omics data.

Pantheon-CLI, our first release of PantheonOS, the AgentOS that re-imagines Science

Haplotype-aware CNV analysis from single-cell RNA-seq

Bayesian Segmentation of Spatial Transcriptomics Data

Integrating GWAS and spatial transcriptomics for spatially resolved mapping of cells associated with human complex traits.

A Toolbox for Spatial Transcriptomics Analysis

a spatial deconvolution method based on deep learning frameworks, which converts bulk transcriptomes into spatially resolved single-cell expression profiles

Open-ST: profile and analyze tissue transcriptomes in 3D with high resolution in your lab

Associated code to the manuscript "Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using high definition spatial profiling"

From geospatial to spatial -omics